Abstract
miRNAs play essential roles in the modulation of cellular functions via degradation and/or translationattenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotateddraft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs inH. roretzihave not been previously studied. We report the prediction of 319 candidateH. roretzimiRNAs, obtained through three complementarymethods. Experimental validation suggests that more than half of these candidate miRNAs are expressed duringembryogenesis. The majority of predictedH. roretzimiRNAs appear specific to ascidians or tunicates, and only 32candidates, belonging to 25 families, are widely conserved across metazoans. Our study presents a comprehensive identification of candidateH. roretzimiRNAs. This resourcewill facilitate the study of the mechanisms for miRNA-controlled gene regulatory networks during ascidiandevelopment. Further, our analysis suggests that the majority ofHalocynthiamiRNAs are specific to ascidianor tunicates, with only a small number of widely conserved miRNAs. This result is consistent with the generalnotion that animal miRNAs are less conserved between taxa than plant ones.